Quality control for BAM files
BamQC depends on the SeqAn core library, version 1.4.2 (https://github.com/seqan/seqan). Please use the 1.4.2 release of SeqAn as no other version will work.
If you put the SeqAn library in a default include directory:
$ git clone https://github.com/DecodeGenetics/BamQC.git
$ cd BamQC
$ make
$ ./bamqualcheck
If you put the SeqAn library in another directory, you will need to edit line 14 of the Makefile and specify the path, e.g.
CXXFLAGS+=-I../libraries/seqan-1.4.2/include
The bamqualcheck program takes as input a BAM file. In addition, the reference genome and an output file are required as options:
$ ./bamqualcheck -r genome.fa -o sample.bamqc sample.bam
If you are using another reference than the human genome or if your chromosomes are not named chr1, chr2, ..., you will need to specify the list of main chromosomes using the option -c, e.g.:
$ ./bamqualcheck -r genome.fa -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y -o sample.bamqc sample.bam
If your library has insert sizes exceeding 1000 bps, you need to increase the maximum in the insert size histogram using the option -i, e.g.
$ ./bamqualcheck -r genome.fa -i 3000 -o sample.bamqc sample.bam
The program output is a text file where each line corresponds to one count or hisotgram of counts.
If you are interested in only one specific measure, it can easily be extracted on the command line using grep, e.g.
$ grep insert_size_histogram sample.bamqc